It isn't that you made her uncomfortable, it's that you failed to fully make her comfortable. If you want a more technical explanation, read the spoiler.
There are a few things you can do to test if Primrose has enough of a crush on the player to get that scene. If, when you first tell Primrose she's being investigated, she gives you a kiss, then you'll get the scene. If, after you work, you ask Primrose if she'll pay you with a kiss and she gets flustered, you'll get that scene. If you ask Primrose for her panties and she gives them to you, you'll get that scene.